anvi-script-filter-hmm-hits-table

Filter weak HMM hits from a given contigs database using a domain hits table reported by anvi-run-hmms..

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Authors

Can consume

contigs-db hmm-source hmm-hits

Can provide

hmm-hits

Usage

This program allows you to remove low quality HMM alignments from a hmm-source in a contigs-db with HMM alignment parameters such as model-coverage (query-coverage) and gene-coverage (target-coverage), or by removing partial genes (i.e., genes that are not partial and that start with a start codon and end with a stop codon). Briefly, the program will remove all records from an hmm-source in the hmm-hits, then import a new hmm-hits table into the contigs-db that was filtered to your specifications.

Filter with HMM alignment parameters

Similar to query coverage in BLAST, we can also use HMM alignment coverage to help determine if an hmm-hit is homologous. A small coverage value means only a small proportion of the query/target is aligning. Before anvi’o can filter out hmm-hits with alignment coverage, you must run anvi-run-hmms and report a domain hits table by including --domain-hits-table flag in your command:

After the command above, your HMM hits will be stored in your contigs-db as usual. However, with the domain hits table, you can filter out hits from your contigs-db using thresholds for model or gene coverage of each hit i.e. you can filter out hmm-hits where the profile HMM and gene align well to each other.

For example, following the command above, the command below will remove hmm-hits from your contigs-db for profile HMMs that had less than 90% coverage of the target genes:

HMMs with multiple hits to one gene

Some HMM profiles align multiple times to the same gene at different coordinates. The program anvi-script-filter-hmm-hits-table by default will use only one of those domain hits table records which could represent very little alignment coverage. To combine the domain hits table records into one hit and thus increasing alignment coverage, use the parameter --merge-partial-hits-within-X-nts. Briefly, if you give the parameter --merge-partial-hits-within-X-nts 300, anvi-script-filter-hmm-hits-table will merge all hits to the same gene in the domain hits table that have coordinates within 300 nucleotides of each other.

The input domtblout file for anvi-script-filter-hmm-hits-table will be saved as hmm.domtable.orig and the output, filtered version will be saved as hmm.domtable. If you decide to change the coverage filtering threshold or --merge-partial-hits-within-X-nts, be sure to change the path for --domain-hits-table to hmm.domtable.orig.

Filter out hmm-hits from partial genes

HMMs are able to detect partial genes (i.e., genes that are not partial and that start with a start codon and end with a stop codon) with good alignment coverage and homology statistics. However, partial genes can lead to spurious phylogenetic branches and/or inflate the number of observed populations or functions in a given set of genomes/metagenomes. Using --filter-out-partial-gene-calls, you can remove partial gene hmm-hits.

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Additional Resources

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.